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Compute the number of radiology tests per encounter

n_imaging.Rd

n_imaging returns the number of radiology tests for hospital admission.

Usage

n_imaging(dbcon, cohort, exclude_ed = FALSE)

Arguments

dbcon

(DBIConnection)
A database connection to any GEMINI database. Only DBI connection is accepted as odbc connection may cause connection issues in certain environment.

cohort

(data.frame or data.table) Cohort table with all relevant encounters of interest, where each row corresponds to a single encounter. Must contain GEMINI Encounter ID (genc_id).

exclude_ed

(logical) Whether to exclude tests in emergency department. When set to TRUE, tests performed in ED (testing time before admission time) will not be counted. When set to FALSE, tests will not be filtered by time and all tests in radiology table will be counted. Please be aware that this may include tests before triage time, tests after discharge time, and tests without testing time.

Tests in ED are defined as ordered_date_time earlier than admission_date_time. When ordered_date_time is not available, performed_date_time is used instead.

Value

data.table with the same number of rows as input cohort, with additional derived numeric fields labelled as "n_img_xray_derived", "n_img_ct_derived", "n_img_mri_derived", "n_img_us_derived", "n_img_other_derived", "n_img_int_derived" and "n_img_ct_mri_us_derived".

Details

This function takes a list of admissions and a GEMINI database connection to generate numeric fields counting the number of different radiology tests for each admission.

Imaging table in the database should include field that classifies each test into below 7 categories.

  • 1 : X-Ray

  • 2 : CT

  • 3 : MRI

  • 4 : Ultrasound

  • 5 : Other

  • 6 : Interventional radiology procedures

  • 7 : Echo (Excluded)

Therefore, this function should be run after some standardization efforts on imaging table (performed by GEMINI team). Currently, the number of advanced radiology tests is one of the performance metrics in MyPracticeReport. CT, MRI and Ultrasound are considered advance imaging tests, which can be retrieved by the derived variable (n_img_ct_mri_us_derived).

Note

Currently, the function does not take radiology data coverage into account. For patients without imaging tests, the function will return 0 in result columns. User should check radiology data coverage and decide whether the imputed 0s are appropriate or not.

Warning

Function returns data.table with id field and several numeric fields. By design, function will not return any NA values. When one tries to left-join the output of this function with another table (another list of admissions in the left), make sure list of admissions (or patient) aligns in both tables.